X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 10% PEG 6000, 100mM TRIS pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.35 α = 90
b = 89.57 β = 104.95
c = 94.51 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-08-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9787 APS 19-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.85 50 98.8 0.049 -- -- 4.2 139309 71108 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.85 1.92 90.1 0.432 -- -- 3.2 12698

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.85 30.0 -- 0.0 69079 69079 3497 100.0 0.173 -- 0.171 0.215 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.85 1.898 3870 199 3671 0.259 0.302 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.546
Anisotropic B[1][1] -0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.85
Anisotropic B[2][2] -1.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.43
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.251
r_dihedral_angle_1_deg 7.037
r_symmetry_vdw_refined 0.192
r_symmetry_hbond_refined 0.21
r_bond_other_d 0.002
r_mcbond_it 1.316
r_angle_refined_deg 2.124
r_scbond_it 3.784
r_symmetry_vdw_other 0.3
r_bond_refined_d 0.028
r_chiral_restr 0.144
r_gen_planes_other 0.013
r_nbd_refined 0.232
r_xyhbond_nbd_refined 0.18
r_mcangle_it 2.161
r_nbtor_other 0.1
r_scangle_it 5.027
r_gen_planes_refined 0.013
r_angle_other_deg 1.113
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5129
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 517

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.09
RESOLVE phasing version: 2.09
REFMAC refinement version: 5.1.24
PDB_EXTRACT data extraction version: 2.000
HKL-2000 data reduction